Long ago, all humans lived beneath the sea. However, some people preferred the surface and abandoned living underwater permanently. As a consequence, they were stripped of their god-given protection called "Ena" which allowed them to breathe underwater. Over time, the rift between the denizens of the sea and of the surface widened, although contact between the two peoples still existed. Nagi no Asu kara follows the story of Hikari Sakishima and Manaka Mukaido, along with their childhood friends Chisaki Hiradaira and Kaname Isaki, who are forced to leave the sea and attend a school on the surface. There, the group also meets Tsumugu Kihara, a fellow student and fisherman who loves the sea. Hikari and his friends' lives are bound to change as they have to deal with the deep-seated hatred and discrimination between the people of sea and of the surface, the storms in their personal lives, as well as an impending tempest which may spell doom for all who dwell on the surface.

The story follows the school life of the three girls, Yuzuko, Yukari, and Yui, who join their high school's Data Processing Club. The odd friendship between the three make for wacky humor in even the most mundane of events.

Rokurou "Rock" Okajima has joined the Lagoon Company, a pirate mercenary group which operates out of Roanapur, Thailand. Despite his initial protests, this filthy slum of depraved souls and merciless criminals now serves as the former salaryman's home. Stranded, with nothing left of his past life but the clothes on his back and his inner morality, Rock is forced to perform jobs alongside the other members of the Lagoon crew. Berated for his lack of spine as he wades through the underbelly of society, he must decide whether to continue on amidst the gunfire and ruthlessness or risk everything he has in an attempt to be free. Whether he chooses the comfort of a familiar land or the freedom of being an outlaw, his decision will have lasting consequences on the crew who gave him a home.

Within Thailand is Roanapur, a depraved, crime-ridden city where not even the authorities or churches are untouched by the claws of corruption. A haven for convicts and degenerates alike, the city is notorious for being the center of illegal activities and operations, often fueled by local crime syndicates. Enter Rokurou Okajima, an average Japanese businessman who has been living a dull and monotonous life, when he finally gets his chance for a change of pace with a delivery trip to Southeast Asia. His business trip swiftly goes downhill as Rokurou is captured by a mercenary group operating in Roanapur, called Black Lagoon. The group plans to use him as a bargaining chip in negotiations which ultimately failed. Now abandoned and betrayed by his former employer, Rokurou decides to join Black Lagoon. In order to survive, he must quickly adapt to his new environment and prepare himself for the bloodshed and tribulation to come. A non-stop, high-octane thriller, Black Lagoon delves into the depths of human morality and virtue. Witness Rokurou struggling to keep his values and philosophies intact as he slowly transforms from businessman to ruthless mercenary.